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Intraspecific variation of organisms is of great importance to correctly carry out taxonomic work, which is a prerequisite for key disciplines in paleontology such as community paleoecology, biostratigraphy, and biogeography. However, intraspecific variation is rarely studied in ectocochleate cephalopods (ammonoids and nautiloids), for which an excessive number of taxa was established during the past centuries. Because intraspecific variation of fossilized organisms suffers from various biases (time averaging and taphonomy), an extant example is needed for actualistic comparison. We applied 3D morphometry to 93 specimens of Nautilus pompilius from three different geographic populations. This data set was used to examine the intraspecific variation throughout ontogeny in detail. Although there are slight differences between the populations as well as some measurement biases, a common pattern of intraspecific variation appears to be present. High variation in morphometric variables appears early in ontogeny and then decreases gradually in the following ontogenetic stages. Subsequently, the variation shows an increase again before maturity until a sharp increase or decrease occurs toward the end of ontogeny. Comparison with intraspecific variation of ammonoids and belemnites illustrated that some groups have ontogenetic patterns of intraspecific variation that are similar to that of N. pompilius. This implies that the abovementioned ontogenetic pattern of intraspecific variation might be common in some major cephalopod clades.